Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MED12

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Colon carcinoma
cell line
HCT116
crispr knockout
CDK8/19 KO-C1
chip antibody
MED12; A300-774A - M (Bethyl Laboratories)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on a NexSeq 500 (100 bp, single end reads).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
46804504
Reads aligned (%)
95.3
Duplicates removed (%)
35.1
Number of peaks
4362 (qval < 1E-05)

hg19

Number of total reads
46804504
Reads aligned (%)
94.5
Duplicates removed (%)
36.6
Number of peaks
4221 (qval < 1E-05)

Base call quality data from DBCLS SRA